Evolution of Cis-Regulatory Elements and Regulatory Networks in Duplicated Genes of Arabidopsis
Evolution of Cis-Regulatory Elements and Regulatory Networks in Duplicated Genes of Arabidopsis
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DOI：
10.1104/pp.15.00717
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发表时间：
2015-12-01
期刊：
影响因子：
7.4
通讯作者：
Adams, Keith L.
中科院分区：
文献类型：
--
作者：
Arsovski, Andrej A.;Pradinuk, Julian;Adams, Keith L.
植物基因组包含大量重复的基因，这些基因有助于新功能的进化。在复制之后，基因的编码序列和表达模式可能会出现差异。顺式调控元件格局的变化会导致基因表达模式的变化。最近开发的高通量方法可以在全基因组范围内识别潜在的顺式调控元件。在这里，我们使用最近的DNase I测序确定的单碱基对分辨率的顺式调控结合位点(Footprint)的综合数据集来比较拟南芥(Arabiopsis Thaliana)复制基因对中的结合位点和网络连通性。我们发现，复制的基因对在其顺式调控元件结构上有很大的差异，导致调控网络连通性的变化。全基因组复制体(WGD)在其启动子中由潜在调控蛋白留下的足迹大约是串联复制体(TD)的两倍。与TD相比，WGD之间的平均足迹差异更大。这些足迹反过来又导致了WGD和其他基因之间更多的调控网络连接，形成了比TD所显示的更密集、更复杂的调控网络。当比较重复之间的调控连接时，WGD有更多的两个基因在其网络连接中部分或完全分叉的对，但没有网络连接的基因比TDS少。有证据表明，与年长的复制品相比，较年轻的TD和WGD具有较少的独特连接。这项研究对复制基因中顺式调控元件的进化和网络分歧提供了见解。
Plant genomes contain large numbers of duplicated genes that contribute to the evolution of new functions. Following duplication, genes can exhibit divergence in their coding sequence and their expression patterns. Changes in the cis-regulatory element landscape can result in changes in gene expression patterns. High-throughput methods developed recently can identify potential cis-regulatory elements on a genome-wide scale. Here, we use a recent comprehensive data set of DNase I sequencing-identified cis-regulatory binding sites (footprints) at single-base-pair resolution to compare binding sites and network connectivity in duplicated gene pairs in Arabidopsis (Arabidopsis thaliana). We found that duplicated gene pairs vary greatly in their cis-regulatory element architecture, resulting in changes in regulatory network connectivity. Whole-genome duplicates (WGDs) have approximately twice as many footprints in their promoters left by potential regulatory proteins than do tandem duplicates (TDs). The WGDs have a greater average number of footprint differences between paralogs than TDs. The footprints, in turn, result in more regulatory network connections between WGDs and other genes, forming denser, more complex regulatory networks than shown by TDs. When comparing regulatory connections between duplicates, WGDs had more pairs in which the two genes are either partially or fully diverged in their network connections, but fewer genes with no network connections than the TDs. There is evidence of younger TDs and WGDs having fewer unique connections compared with older duplicates. This study provides insights into cis-regulatory element evolution and network divergence in duplicated genes.